SILACFiltering.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Lars Nilse $
// $Authors: Steffen Sass, Holger Plattfaut, Bastian Blank $
// --------------------------------------------------------------------------

#ifndef OPENMS_FILTERING_DATAREDUCTION_SILACFILTERING_H
#define OPENMS_FILTERING_DATAREDUCTION_SILACFILTERING_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/PeakWidthEstimator.h>

#include <gsl/gsl_interp.h>
#include <gsl/gsl_spline.h>
#include <list>
#include <map>
#include <vector>

namespace OpenMS
{
  class SILACFilter;

  class OPENMS_DLLAPI SILACFiltering :
    public ProgressLogger
  {
public:
    typedef std::vector<SILACFilter> Filters;

    Filters filters_;

    class OPENMS_DLLAPI SpectrumInterpolation
    {
private:
      gsl_interp_accel * current_;
      gsl_spline * spline_;

public:
      SpectrumInterpolation(const MSSpectrum<> &, const SILACFiltering &);
      ~SpectrumInterpolation();

      DoubleReal operator()(DoubleReal mz) const
      {
        return gsl_spline_eval(spline_, mz, current_);
      }

    };

private:
    DoubleReal intensity_cutoff_;

    MSExperiment<Peak1D> & exp_;

    MSExperiment<Peak1D> picked_exp_;

    MSExperiment<Peak1D> picked_exp_seeds_;

    const String debug_filebase_;

    void pickSeeds_();

    void filterSeeds_();

public:

    const PeakWidthEstimator::Result peak_width;

    SILACFiltering(MSExperiment<Peak1D> & exp, const PeakWidthEstimator::Result &, const DoubleReal intensity_cutoff, const String debug_filebase_ = "");

    void addFilter(SILACFilter & filter);

    void filterDataPoints();

    struct BlacklistEntry
    {
      DRange<2> range;
      Int charge;
      std::vector<DoubleReal> mass_separations;
      DoubleReal relative_peak_position;
    };

    std::multimap<DoubleReal, BlacklistEntry> blacklist;
  };
}

#endif /* SILACFILTERING_H_ */